Add a transparent image on top of a material [duplicate 2]
UPDATED
I totally misunderstood your problem in my first answer so here is an update. 
Your problem wasnt the transparency obviously, but the UV map itself. 
As I checked your file (ninja28) It was like having two UV maps one over each other or maybe just overlaps on the same channel. I dont know what caused this, but if you did a remapping (even by using the mapping node or unwrapping the mesh again - I did both) it should work fine.



And Here is your (edited) file: